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- PDB-4wg2: P411BM3-CIS T438S I263F regioselective C-H amination catalyst -

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Basic information

Entry
Database: PDB / ID: 4wg2
TitleP411BM3-CIS T438S I263F regioselective C-H amination catalyst
ComponentsBifunctional P-450/NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / P411BM3-CIS / engineering / catalysis
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.66 Å
AuthorsHyster, T.K. / Farwell, C.C. / Buller, A.R. / McIntosh, J.A. / Arnold, F.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Enzyme-controlled nitrogen-atom transfer enables regiodivergent C-h amination.
Authors: Hyster, T.K. / Farwell, C.C. / Buller, A.R. / McIntosh, J.A. / Arnold, F.H.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: diffrn_detector / entity_name_com ...diffrn_detector / entity_name_com / entity_src_gen / pdbx_database_related / pdbx_database_status / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional P-450/NADPH-P450 reductase
B: Bifunctional P-450/NADPH-P450 reductase
C: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,9719
Polymers160,8333
Non-polymers2,1386
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.897, 206.897, 119.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-601-

SO4

21C-601-

SO4

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Components

#1: Protein Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3


Mass: 53611.059 Da / Num. of mol.: 3
Mutation: V78A, F87V, P142S, T175I, A184V, S226R, H236Q, E252G, I263F, T268A, A290V, L353V, I366V, C400S, T438S, E442K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / Production host: Escherichia coli (E. coli)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris/HCl pH = 7, 2.0 M ammonium sulfate, 0.2 M lithium sulfate 12 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.66→40 Å / Num. obs: 70732 / % possible obs: 100 % / Redundancy: 13.8 % / Net I/σ(I): 11

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.66→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 23.476 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23502 3794 5.1 %RANDOM
Rwork0.19663 ---
obs0.19859 70732 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20 Å2
2---0.3 Å20 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.66→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10737 0 144 66 10947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911153
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210430
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.98115178
X-RAY DIFFRACTIONr_angle_other_deg0.745323953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90151367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94724.778519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.915151823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2141554
X-RAY DIFFRACTIONr_chiral_restr0.0890.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112742
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022562
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7543.6215483
X-RAY DIFFRACTIONr_mcbond_other1.7533.6215482
X-RAY DIFFRACTIONr_mcangle_it2.9445.4266845
X-RAY DIFFRACTIONr_mcangle_other2.9445.4266846
X-RAY DIFFRACTIONr_scbond_it1.8953.7655670
X-RAY DIFFRACTIONr_scbond_other1.8853.7585656
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1595.5738315
X-RAY DIFFRACTIONr_long_range_B_refined4.8728.57512592
X-RAY DIFFRACTIONr_long_range_B_other4.8728.57612592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 293 -
Rwork0.347 5080 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4270.07890.05560.3702-0.09470.4028-0.0870.0772-0.0169-0.12170.09730.04730.0794-0.1083-0.01030.2194-0.0667-0.00880.1894-0.00510.123-3.535-33.852-19.706
24.99972.93130.25493.256-0.11940.42920.1894-0.54550.10660.0256-0.25730.06020.0142-0.21210.06790.1643-0.0523-0.01950.2906-0.02630.1196-10.057-22.633-12.347
30.75750.06110.67490.3338-0.07841.3644-0.11770.1188-0.0906-0.11280.0611-0.07810.10470.06110.05660.2122-0.02760.04490.1583-0.02990.14288.035-41.265-17.958
40.58110.25170.04110.61290.56231.1212-0.14960.1331-0.0627-0.05830.06280.02330.1121-0.13780.08680.1835-0.068-0.00420.1792-0.01240.1136-37.272-4.114-34.735
52.14170.12940.27744.40921.35781.4314-0.05570.1238-0.11030.399-0.22230.17560.3181-0.38310.2780.261-0.0950.04310.2444-0.04330.1577-50.734-6.15-28.08
61.02870.62410.4060.41370.42621.317-0.16490.14070.0377-0.10320.09890.00890.00360.01910.0660.2132-0.0315-0.00960.1870.01180.1195-26.3033.719-33.903
70.41360.20230.55950.69280.24560.87380.0471-0.06210.03080.096-0.0988-0.0618-0.0730.0070.05170.1734-0.12440.02060.1996-0.00350.1359-49.236-54.62-32.952
84.7441.9828-0.80282.5723-0.08681.3027-0.2461-0.17290.2855-0.12520.04910.1909-0.1628-0.00170.1970.237-0.1024-0.03780.1499-0.04490.2056-55.329-42.468-37.416
90.56890.43160.35390.72990.43511.59740.1265-0.1128-0.11380.1003-0.1094-0.06850.00270.0406-0.01710.1855-0.0934-0.01710.16390.02770.1639-49.893-68.059-35.493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 169
2X-RAY DIFFRACTION2A170 - 267
3X-RAY DIFFRACTION3A268 - 464
4X-RAY DIFFRACTION4B3 - 172
5X-RAY DIFFRACTION5B173 - 262
6X-RAY DIFFRACTION6B263 - 458
7X-RAY DIFFRACTION7C4 - 172
8X-RAY DIFFRACTION8C173 - 267
9X-RAY DIFFRACTION9C268 - 463

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